Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1229
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13531
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2411 original size:20 final size:20
Alignment explanation
Indices: 2388--2460 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2378 ACAATTCAAA
2388 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2408 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2429 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2449 GTATCGATACAT
1 GTATCGATACAT
2461 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2432 original size:21 final size:21
Alignment explanation
Indices: 2406--2481 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2396 ACATGTTGCA
2406 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2427 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2447 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2468 ATGTATCGATACAT
1 ATGTATCGATACAT
2482 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2439 original size:41 final size:41
Alignment explanation
Indices: 2388--2481 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2378 ACAATTCAAA
*
2388 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2429 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2470 GTATCGATACAT
1 GTATCGATACAT
2482 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2538 original size:13 final size:13
Alignment explanation
Indices: 2520--2545 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2510 TACAGCAAGT
2520 ATGTATCGATACA
1 ATGTATCGATACA
2533 ATGTATCGATACA
1 ATGTATCGATACA
2546 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4723 original size:78 final size:77
Alignment explanation
Indices: 4612--4812 Score: 215
Period size: 78 Copynumber: 2.6 Consensus size: 77
4602 GAGATAATAA
* * * ** * *
4612 CGGGGTTGGAGTGTTCCCTTGAAAATAATGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGT-ATCCCTCGAAAATAACGGGGCTGGAGTATCCCCAATTATGAGAAATCAAT-A
*
4677 -TTAGAAAAAAAAT
64 TTTAGAAAAAAAAC
*
4690 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGCTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTAT-CCCTCGAAAATAACGGGGCTGGAGTATCCCCAATTATGAGAAATCAATA-
* * * *
4755 TTTGGGAATAAAGC
64 TTTAGAAAAAAAAC
* * *
4769 CGGGGTTGGAGTATCCCTCGGAAGTAACGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCCTCGAAAATAACGGGGCTGGAGTATCCC
4813 TGATGAAATA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
77 2 0.02
78 80 0.78
79 21 0.20
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.24
Consensus pattern (77 bp):
CGGGGTTGGAGTATCCCTCGAAAATAACGGGGCTGGAGTATCCCCAATTATGAGAAATCAATATT
TAGAAAAAAAAC
Found at i:4799 original size:27 final size:27
Alignment explanation
Indices: 4769--4839 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
4759 GGAATAAAGC
*
4769 CGGGGTTGGAGTATCCCTCG-GAAGTAA
1 CGGGGTTGGAGTATCCCT-GAGAAATAA
4796 CGGGGTTGGAGTATCCCTGATGAAATAA
1 CGGGGTTGGAGTATCCCTGA-GAAATAA
*
4824 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
4840 TCGATTGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.45
28 21 0.52
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTGAGAAATAA
Found at i:5005 original size:52 final size:52
Alignment explanation
Indices: 4828--5006 Score: 236
Period size: 52 Copynumber: 3.4 Consensus size: 52
4818 AAATAACGAG
* * *
4828 GTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGT-GTTTTGAAAATAAAATCGGA
** * * *
4880 GTTGGAGTATCCCCGATTAAAGG-AAAATTGGTGTTTCGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGTGTTTTGAAAATAAAATCGGA
*
4932 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAAAATAAAATCGGA
*
4984 GTTGGAATATCCCCGATTGTGGA
1 GTTGGAGTATCCCCGATTGTGGA
5007 GAATTGAGAA
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
51 2 0.02
52 97 0.89
53 9 0.08
54 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:7380 original size:13 final size:13
Alignment explanation
Indices: 7362--7387 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7352 ACAAAGATCC
7362 ATGTATCGATACA
1 ATGTATCGATACA
7375 ATGTATCGATACA
1 ATGTATCGATACA
7388 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7383 original size:33 final size:33
Alignment explanation
Indices: 7341--7407 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
7331 AAAATTTTCA
***
7341 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
7374 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
7407 A
1 A
7408 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:7451 original size:19 final size:18
Alignment explanation
Indices: 7427--7494 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
7417 CAGTAGCTAA
7427 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
7446 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
7461 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
7478 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
7495 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:7467 original size:13 final size:13
Alignment explanation
Indices: 7449--7473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7439 ACAATACTTA
7449 TGTATCGATACAT
1 TGTATCGATACAT
7462 TGTATCGATACA
1 TGTATCGATACA
7474 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7471 original size:32 final size:32
Alignment explanation
Indices: 7430--7492 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
7420 TAGCTAATTA
*
7430 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
7462 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
7493 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:7891 original size:20 final size:21
Alignment explanation
Indices: 7831--7904 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
7821 TTCTACAATT
* *
7831 TGTATCGATACAATAAAT-TAA
1 TGTATCGATAC-ATAAGTGAAA
7852 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAGTGAAA
***
7872 TGTATCGATACATGTTTGAAA
1 TGTATCGATACATAAGTGAAA
*
7893 TGTATCAATACA
1 TGTATCGATACA
7905 AAACCATGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 22 0.48
21 24 0.52
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:7898 original size:21 final size:20
Alignment explanation
Indices: 7831--7884 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
7821 TTCTACAATT
* *
7831 TGTATCGATACAATAAATTAA
1 TGTATCGATAC-ATAAGTGAA
7852 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
7872 TGTATCGATACAT
1 TGTATCGATACAT
7885 GTTTGAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:10883 original size:22 final size:22
Alignment explanation
Indices: 10855--10897 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
10845 GTTCATCACA
10855 GTATCGATACATCACTGTTCAT
1 GTATCGATACATCACTGTTCAT
*
10877 GTATCGATACATCACTTTTCA
1 GTATCGATACATCACTGTTCA
10898 CACTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (22 bp):
GTATCGATACATCACTGTTCAT
Found at i:13139 original size:51 final size:52
Alignment explanation
Indices: 13018--13145 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
13008 CCCGATATGA
*
13018 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
**
13070 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATAC-TCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
13121 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
13146 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 32 0.44
52 41 0.56
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
Found at i:13256 original size:13 final size:13
Alignment explanation
Indices: 13238--13275 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
13228 CAAAAAAATA
*
13238 TGTATCGATACCT
1 TGTATCGATACAT
13251 TGTATCGATACAT
1 TGTATCGATACAT
13264 TGTATCGATACA
1 TGTATCGATACA
13276 ACACTTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Done.